PrecisionFDA
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Explore HG002 comparison results
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| Entry | Type | Subtype | Subset | Genotype | F-score | Recall | Precision | Frac_NA | Truth TP | Truth FN | Query TP | Query FP | FP gt | % FP ma | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
1701-1750 / 86044 show all | |||||||||||||||
| astatham-gatk | SNP | * | map_l150_m1_e0 | * | 91.4460 | 84.4686 | 99.6799 | 78.7872 | 25855 | 4754 | 25849 | 83 | 39 | 46.9880 | |
| ghariani-varprowl | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 0.0000 | 0.3982 | 0.0000 | 0.0000 | 19 | 4753 | 0 | 0 | 0 | ||
| ghariani-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 0.0000 | 0.4191 | 0.0000 | 0.0000 | 20 | 4752 | 0 | 0 | 0 | ||
| gduggal-snapplat | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 37.1926 | 25.0079 | 72.5332 | 64.8432 | 1581 | 4741 | 1529 | 579 | 94 | 16.2349 | |
| gduggal-snapplat | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 37.1926 | 25.0079 | 72.5332 | 64.8432 | 1581 | 4741 | 1529 | 579 | 94 | 16.2349 | |
| gduggal-bwaplat | INDEL | I1_5 | * | homalt | 95.8146 | 92.1560 | 99.7758 | 57.5165 | 55688 | 4740 | 55641 | 125 | 99 | 79.2000 | |
| ciseli-custom | SNP | ti | map_l100_m0_e0 | * | 82.2845 | 78.2555 | 86.7509 | 73.7443 | 17037 | 4734 | 17024 | 2600 | 753 | 28.9615 | |
| mlin-fermikit | SNP | ti | map_l125_m1_e0 | homalt | 66.1427 | 57.1480 | 78.4977 | 52.8912 | 6312 | 4733 | 6312 | 1729 | 1647 | 95.2574 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 56.2787 | 41.6430 | 86.7771 | 58.5183 | 3371 | 4724 | 3406 | 519 | 454 | 87.4759 | |
| astatham-gatk | SNP | ti | map_l125_m2_e0 | het | 85.6054 | 75.0000 | 99.7041 | 80.6061 | 14157 | 4719 | 14153 | 42 | 19 | 45.2381 | |
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 77.6657 | 65.6975 | 94.9658 | 82.9333 | 9038 | 4719 | 9036 | 479 | 120 | 25.0522 | |
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 77.6657 | 65.6975 | 94.9658 | 82.9333 | 9038 | 4719 | 9036 | 479 | 120 | 25.0522 | |
| astatham-gatk | SNP | ti | map_l125_m1_e0 | * | 91.1797 | 83.9407 | 99.7852 | 74.5658 | 24624 | 4711 | 24620 | 53 | 29 | 54.7170 | |
| ndellapenna-hhga | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 87.7319 | 87.1393 | 88.3326 | 67.8909 | 31886 | 4706 | 32320 | 4269 | 3693 | 86.5074 | |
| egarrison-hhga | INDEL | D1_5 | * | * | 96.9873 | 96.8033 | 97.1720 | 57.4559 | 142054 | 4691 | 142118 | 4136 | 3666 | 88.6364 | |
| ckim-isaac | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 90.8245 | 87.6365 | 94.2532 | 40.4574 | 33216 | 4686 | 32687 | 1993 | 1737 | 87.1550 | |
| gduggal-snapfb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 75.3642 | 66.6334 | 86.7280 | 50.6405 | 9350 | 4682 | 2640 | 404 | 232 | 57.4257 | |
| gduggal-bwaplat | SNP | * | map_l250_m1_e0 | * | 51.9747 | 35.1703 | 99.5300 | 97.3642 | 2540 | 4682 | 2541 | 12 | 3 | 25.0000 | |
| jpowers-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 31.1683 | 21.1733 | 59.0373 | 57.3384 | 1256 | 4676 | 1251 | 868 | 834 | 96.0829 | |
| gduggal-snapplat | INDEL | I6_15 | * | homalt | 35.4854 | 25.0841 | 60.6230 | 61.9684 | 1565 | 4674 | 1518 | 986 | 436 | 44.2191 | |
| gduggal-bwafb | INDEL | I1_5 | * | * | 97.8814 | 96.8991 | 98.8838 | 56.3942 | 145992 | 4672 | 146789 | 1657 | 1400 | 84.4900 | |
| anovak-vg | SNP | tv | HG002complexvar | het | 97.4369 | 96.9012 | 97.9786 | 22.5474 | 146063 | 4671 | 144347 | 2978 | 2196 | 73.7408 | |
| egarrison-hhga | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 87.8352 | 87.2704 | 88.4074 | 67.9175 | 31934 | 4658 | 32274 | 4232 | 3738 | 88.3270 | |
| ciseli-custom | INDEL | I1_5 | * | het | 91.4560 | 94.1106 | 88.9472 | 61.0454 | 74385 | 4655 | 74801 | 9295 | 7503 | 80.7208 | |
| gduggal-snapplat | INDEL | D1_5 | HG002complexvar | het | 82.2897 | 77.5921 | 87.5928 | 61.7499 | 16112 | 4653 | 18878 | 2674 | 302 | 11.2939 | |
| jmaeng-gatk | SNP | ti | map_l125_m0_e0 | * | 77.0171 | 63.5715 | 97.6758 | 88.7194 | 8113 | 4649 | 8111 | 193 | 22 | 11.3990 | |
| ckim-gatk | SNP | ti | map_l125_m0_e0 | * | 77.0822 | 63.5950 | 97.8298 | 88.5344 | 8116 | 4646 | 8114 | 180 | 23 | 12.7778 | |
| anovak-vg | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 56.5143 | 51.2341 | 63.0078 | 48.1760 | 4878 | 4643 | 6033 | 3542 | 2746 | 77.5268 | |
| gduggal-snapfb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 79.1914 | 73.9716 | 85.2037 | 51.7929 | 13181 | 4638 | 24318 | 4223 | 1294 | 30.6417 | |
| gduggal-bwavard | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 0.0000 | 0.2582 | 0.0000 | 0.0000 | 12 | 4635 | 0 | 0 | 0 | ||
| gduggal-bwafb | INDEL | I6_15 | * | * | 87.8626 | 81.3399 | 95.5225 | 40.4474 | 20191 | 4632 | 21206 | 994 | 970 | 97.5855 | |
| jpowers-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 0.0000 | 0.3228 | 0.0000 | 0.0000 | 15 | 4632 | 0 | 0 | 0 | ||
| ghariani-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 0.0000 | 0.3873 | 0.0000 | 0.0000 | 18 | 4629 | 0 | 0 | 0 | ||
| gduggal-bwaplat | SNP | ti | map_l150_m0_e0 | * | 58.2240 | 41.2034 | 99.2037 | 94.0967 | 3239 | 4622 | 3239 | 26 | 11 | 42.3077 | |
| astatham-gatk | SNP | * | map_l150_m1_e0 | het | 86.2499 | 76.0872 | 99.5460 | 82.9944 | 14697 | 4619 | 14691 | 67 | 26 | 38.8060 | |
| qzeng-custom | SNP | ti | map_l125_m0_e0 | * | 76.6106 | 63.8536 | 95.7374 | 88.8132 | 8149 | 4613 | 8108 | 361 | 304 | 84.2105 | |
| astatham-gatk | SNP | ti | map_l125_m1_e0 | het | 85.4533 | 74.7728 | 99.6933 | 79.6242 | 13658 | 4608 | 13654 | 42 | 19 | 45.2381 | |
| gduggal-bwaplat | INDEL | D1_5 | HG002complexvar | * | 91.7545 | 85.9392 | 98.4139 | 61.1958 | 28115 | 4600 | 28045 | 452 | 321 | 71.0177 | |
| gduggal-bwavard | SNP | * | HG002compoundhet | * | 84.7137 | 82.2128 | 87.3715 | 45.7405 | 21229 | 4593 | 20991 | 3034 | 2565 | 84.5419 | |
| jmaeng-gatk | SNP | ti | * | het | 99.6655 | 99.6418 | 99.6893 | 25.0371 | 1277299 | 4592 | 1277249 | 3981 | 127 | 3.1902 | |
| egarrison-hhga | INDEL | D6_15 | * | * | 86.6592 | 82.4007 | 91.3819 | 53.7350 | 21500 | 4592 | 21631 | 2040 | 1771 | 86.8137 | |
| ckim-isaac | INDEL | * | HG002complexvar | het | 92.2376 | 90.0654 | 94.5171 | 48.6355 | 41621 | 4591 | 40028 | 2322 | 1017 | 43.7984 | |
| gduggal-bwavard | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 32.9929 | 22.6568 | 60.6716 | 52.9029 | 1344 | 4588 | 1319 | 855 | 827 | 96.7251 | |
| ckim-vqsr | SNP | * | map_l250_m2_e1 | * | 59.3854 | 42.5817 | 98.0963 | 97.1254 | 3401 | 4586 | 3401 | 66 | 0 | 0.0000 | |
| gduggal-bwaplat | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 68.9830 | 54.5121 | 93.9135 | 78.7818 | 5491 | 4582 | 5493 | 356 | 149 | 41.8539 | |
| gduggal-bwaplat | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 90.3847 | 84.0798 | 97.7117 | 90.1711 | 24141 | 4571 | 24169 | 566 | 135 | 23.8516 | |
| gduggal-bwaplat | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 90.3847 | 84.0798 | 97.7117 | 90.1711 | 24141 | 4571 | 24169 | 566 | 135 | 23.8516 | |
| ndellapenna-hhga | INDEL | D6_15 | * | * | 86.5914 | 82.4889 | 91.1232 | 54.1208 | 21523 | 4569 | 21701 | 2114 | 1783 | 84.3425 | |
| gduggal-snapplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 52.7132 | 36.3814 | 95.6522 | 52.4661 | 2610 | 4564 | 2618 | 119 | 102 | 85.7143 | |
| gduggal-snapvard | INDEL | * | HG002complexvar | het | 85.1014 | 90.1233 | 80.6095 | 59.0444 | 41646 | 4564 | 51233 | 12324 | 8222 | 66.7154 | |